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Publication

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution.

Cancer cell | 2020

Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profile single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from pre-neoplastic hyperplasia to adenocarcinoma. The diversity of transcriptional states increases over time and is reproducible across tumors and mice. Cancer cells progressively adopt alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts display high capacity for differentiation and proliferation. The HPCS program is associated with poor survival across human cancers and demonstrates chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.

Pubmed ID: 32707077 RIS Download

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Associated grants

Agency: Medical Research Council, United Kingdom
Id: MC_PC_17230
Agency: NCI NIH HHS, United States
Id: R00 CA187317
Agency: NCI NIH HHS, United States
Id: T32 CA009207
Agency: NCI NIH HHS, United States
Id: K99 CA187317
Agency: NCI NIH HHS, United States
Id: P30 CA014051
Agency: NCI NIH HHS, United States
Id: P30 CA008748
Agency: NCI NIH HHS, United States
Id: U01 CA196405
Agency: NIGMS NIH HHS, United States
Id: T32 GM007287
Agency: Medical Research Council, United Kingdom
Id: MC_PC_12009
Agency: Howard Hughes Medical Institute, United States
Agency: NCI NIH HHS, United States
Id: P01 CA042063
Agency: NCI NIH HHS, United States
Id: P30 CA016086

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This is a list of tools and resources that we have found mentioned in this publication.

SAMTOOLS (tool)

RRID:SCR_002105

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

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CRAN (tool)

RRID:SCR_003005

Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

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Mouse Genome Informatics (MGI) (tool)

RRID:SCR_006460

International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

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Subread (tool)

RRID:SCR_009803

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

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Atac (tool)

RRID:SCR_015980

Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.

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